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Skácel J, Djukic S, Baszczyňski O, Kalčic F, Bílek T, Chalupský K, Kozák J, Dvořáková A, Tloušt'ová E, Král'ová Z, Šmídková M, Voldřich J, Rumlová M, Pachl P, Brynda J, Vučková T, Fábry M, Snášel J, Pichová I, Řezáčová P, Mertlíková-Kaiserová H, Janeba Z. Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors. J Med Chem 2023; 66:6652-6681. [PMID: 37134237 DOI: 10.1021/acs.jmedchem.2c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Purine nucleoside phosphorylase (PNP) is a well-known molecular target with potential therapeutic applications in the treatment of T-cell malignancies and/or bacterial/parasitic infections. Here, we report the design, development of synthetic methodology, and biological evaluation of a series of 30 novel PNP inhibitors based on acyclic nucleoside phosphonates bearing a 9-deazahypoxanthine nucleobase. The strongest inhibitors exhibited IC50 values as low as 19 nM (human PNP) and 4 nM (Mycobacterium tuberculosis (Mt) PNP) and highly selective cytotoxicity toward various T-lymphoblastic cell lines with CC50 values as low as 9 nM. No cytotoxic effect was observed on other cancer cell lines (HeLa S3, HL60, HepG2) or primary PBMCs for up to 10 μM. We report the first example of the PNP inhibitor exhibiting over 60-fold selectivity for the pathogenic enzyme (MtPNP) over hPNP. The results are supported by a crystallographic study of eight enzyme-inhibitor complexes and by ADMET profiling in vitro and in vivo.
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Affiliation(s)
- Jan Skácel
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Stefan Djukic
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Faculty of Science, Charles University in Prague, Hlavova 2030/8, Prague 2 12843, Czech Republic
| | - Filip Kalčic
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Tadeáš Bílek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Karel Chalupský
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jaroslav Kozák
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Alexandra Dvořáková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Eva Tloušt'ová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Zuzana Král'ová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Faculty of Science, Charles University in Prague, Hlavova 2030/8, Prague 2 12843, Czech Republic
| | - Markéta Šmídková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jan Voldřich
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Michaela Rumlová
- University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Tereza Vučková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Science, Vídeňská 1083, Prague 14220, Czech Republic
| | - Jan Snášel
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
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Khandazhinskaya A, Fateev I, Konstantinova I, Esipov R, Polyakov K, Seley-Radtke K, Kochetkov S, Matyugina E. Synthesis of New 5′-Norcarbocyclic Aza/Deaza Purine Fleximers - Noncompetitive Inhibitors of E.coli Purine Nucleoside Phosphorylase. Front Chem 2022; 10:867587. [PMID: 35601551 PMCID: PMC9114674 DOI: 10.3389/fchem.2022.867587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
A new series of flexible 5′-norcarbocyclic aza/deaza-purine nucleoside analogs were synthesized from 6-oxybicyclo[3.1.0.]hex-2-ene and pyrazole-containing fleximer analogs of heterocyclic bases using the Trost procedure. The compounds were evaluated as potential inhibitors of E. coli purine nucleoside phosphorylase. Analog 1-3 were found to be noncompetitive inhibitors with inhibition constants of 14–24 mM. From the data obtained, it can be assumed that the new 5′-norcarbocyclic nucleoside analogs interact with the active site of the PNP like natural heterocyclic bases. But at the same time the presence of a cyclopentyl moiety with 2′ and 3′ hydroxyls is necessary for the inhibitory properties, since compounds 8–10, without those groups did not exhibit an inhibitory effect under the experimental conditions.
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Affiliation(s)
| | - Ilja Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Polyakov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Katherine Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, United States
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Elena Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Elena Matyugina,
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Kaspar F, Wolff DS, Neubauer P, Kurreck A, Arcus VL. pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius. Biochemistry 2021; 60:1573-1577. [PMID: 33955225 DOI: 10.1021/acs.biochem.1c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Enzyme-catalyzed reactions sometimes display curvature in their Eyring plots in the absence of denaturation, indicative of a change in activation heat capacity. However, the effects of pH and (de)protonation on this phenomenon have remained unexplored. Herein, we report a kinetic characterization of the thermophilic pyrimidine nucleoside phosphorylase from Geobacillus thermoglucosidasius across a two-dimensional working space covering 35 °C and 3 pH units with two substrates displaying different pKa values. Our analysis revealed the presence of a measurable activation heat capacity change ΔCp⧧ in this reaction system, which showed no significant dependence on medium pH or substrate charge. Our results further describe the remarkable effects of a single halide substitution that has a minor influence on ΔCp⧧ but conveys a significant kinetic effect by decreasing the activation enthalpy, causing a >10-fold rate increase. Collectively, our results present an important piece in the understanding of enzymatic systems across multidimensional working spaces where the choice of reaction conditions can affect the rate, affinity, and thermodynamic phenomena independently of one another.
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Affiliation(s)
- Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Darian S Wolff
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Vickery L Arcus
- Te Aka Ma̅tuatua-School of Science, Te Whare Wa̅nanga o Waikato-University of Waikato, Hamilton 3240, New Zealand
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